This is my blog. Glad you like it. I used yEd for the dependency graphs. There's a lot of detail on how I did it in the first segment: http://thewebsiteisdown.com/twidblog/puzzle-dependency-graph.... Also available here in case my site goes down again (http://www.gamasutra.com/blogs/JoshuaWeinberg/20160502/27010...).

I can't see all of them since the site is down, but it looks like they could be from yEd / yFiles: https://www.yworks.com/products/yed